Statistical Inference of Associations between Microbial Communities And host phenoTypes

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Documentation for package ‘SIAMCAT’ version 1.0.0

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SIAMCAT-package SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes
accessSlot Universal slot accessor function for siamcat-class.
add.meta.pred Add metadata as predictors
assign-data_split Assign a new data_split object to 'x'
assign-eval_data Assign a new eval_data object to 'x'
assign-features Assign a new otu_table object to 'x' features slot
assign-label Assign a new label object to 'x'
assign-meta Assign a new sam_data object to 'x'
assign-model_list Assign a new model_list object to 'x'
assign-norm_param Assign a new norm_param object to 'x'
assign-orig_feat Assign a new otu_table object to 'x' orig_feat slot
assign-physeq Assign a new phyloseq object to 'x'
assign-pred_matrix Assign a new pred_matrix object to 'x'
check.associations Check and visualize associations between features and classes
check.confounders Check for potential confounders in the metadata
create.data.split Split a dataset into training and a test sets.
data_split Retrieve a data_split-class object from object.
data_split-class The S4 class for storing data splits
data_split-method Retrieve a data_split-class object from object.
data_split<- Assign a new data_split object to 'x'
data_split<--method Assign a new data_split object to 'x'
evaluate.predictions Evaluate prediction results
eval_data Retrieve eval_data from object.
eval_data-class The S4 class for storing evaluation data.
eval_data-method Retrieve eval_data from object.
eval_data<- Assign a new eval_data object to 'x'
eval_data<--method Assign a new eval_data object to 'x'
features Retrieve a otu_table-class object from object.
features-method Retrieve a otu_table-class object from object.
features<- Assign a new otu_table object to 'x' features slot
features<--method Assign a new otu_table object to 'x' features slot
filter.features Perform unsupervised feature filtering.
filter.label Filter samples from 'siamcat@label'
get.features.matrix get.features.matrix
get.orig_feat.matrix get.orig_feat.matrix
label Retrieve a label-class object from object.
label-class The S4 class for storing label info.
label-method Retrieve a label-class object from object.
label<- Assign a new label object to 'x'
label<--method Assign a new label object to 'x'
make.predictions Make predictions on a test set
meta Retrieve a sample_data-class object from object.
meta-method Retrieve a sample_data-class object from object.
meta<- Assign a new sam_data object to 'x'
meta<--method Assign a new sam_data object to 'x'
model.evaluation.plot Model Evaluation Plot
model.interpretation.plot Model Interpretation Plot
models Retrieve list of models from object.
models-method Retrieve model_list-class from object.
models-method Retrieve list of models from object.
model_list Retrieve model_list-class from object.
model_list-class The S4 class for storing models.
model_list-method Retrieve model_list-class from object.
model_list<- Assign a new model_list object to 'x'
model_list<--method Assign a new model_list object to 'x'
model_type Retrieve model_type from object.
model_type-method Retrieve model_list-class from object.
model_type-method Retrieve model_type from object.
normalize.features Perform feature normalization
norm_param Retrieve norm_param from object.
norm_param-method Retrieve norm_param from object.
norm_param<- Assign a new norm_param object to 'x'
norm_param<--method Assign a new norm_param object to 'x'
orig_feat Retrieve a otu_table-class object from orig_feat slot.
orig_feat-class The S4 class for storing original features info.
orig_feat-method Retrieve a label-class object from object.
orig_feat-method Retrieve a otu_table-class object from orig_feat slot.
orig_feat<- Assign a new otu_table object to 'x' orig_feat slot
orig_feat<--method Assign a new otu_table object to 'x' orig_feat slot
physeq Retrieve a phyloseq-class object from object.
physeq-method Retrieve a phyloseq-class object from object.
physeq<- Assign a new phyloseq object to 'x'
physeq<--method Assign a new phyloseq object to 'x'
pred_matrix Retrieve pred_matrix from object.
pred_matrix-class The S4 class for storing label info.
pred_matrix-method Retrieve pred_matrix from object.
pred_matrix<- Assign a new pred_matrix object to 'x'
pred_matrix<--method Assign a new pred_matrix object to 'x'
read.features Read feature file
read.labels Read labels file
read.meta Read metadata file
reset.features reset.features
select.samples Select samples based on metadata
SIAMCAT SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes
siamcat siamcat
siamcat-class The S4 class for storing taxa-abundance information and models.
siamcat_example Documentation for the example siamcat object in the data folder
train.model Model training
validate.data Validate samples in labels, features, and metadata